Hi,
In IPsec configuration section under Site to Site GRE tunnel over IPsec (IKEv2) using DNS
is this configuration in GRE IPsec Tunnel Mode or GRE IPsec Transport Mode?

Transport Mode

But both IPSec and Gre are Layer 3 protocols?
If we want broadcast to past over vpn, we need to use L2TP over IPsec?

i'm not sure if i understand u

What protocols best fit to securely connect same networks over public network?

Transport Mode

It will be transport mode when both endpoints directly have a public IP address.
When there is NAT in front of the MikroTik router at one end, it will be tunnel mode (because IPsec transport mode does not support NAT).

What protocols best fit to securely connect same networks over public network?

GRE/IPsec is a good choice. That is completely unrelated to your first question.

Yes, it is another question. IPsec and Gre doesn't connect same networks?

I don't understand you either. Maybe you are difficult to understand.

Which protocols can do this?

how u mean , whois protocol?

just follow the e.g.
establish the tunnel, which is the main ting.

once u do that u have two option to reach other end
1. /ip ipsec policy (more advanced)
2. /ip route (basic)

I think he wants to extend a single LAN across two physical locations.

For this EOIP is the only real method:

https://help.mikrotik.com/docs/display/ROS/EoIP

Performance depends on CPU though. You can have very mixed and sometimes disappointing results with EOIP.

ok, EoIP in this case will do the job.
Just one note, be careful of 42 byte overhead.

I prefer to play with BCP , but yes test it, and see how it goes.

user this ping x.x.x.x size=mtu_size do-not-fragment, if u get any issues. Good luck!!

BCP has me curious - have you a quick example?